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added more docstrings for blast.py
2009-07-16
Chr
i
stopher Lee
a
d
ded more docstring
s
for bl
a
st
.
py
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
remo
v
ed old
Blas
t
xMa
p
p
ing code
commit
|
commitdiff
|
tree
2009-07-16
Christophe
r
L
e
e
new, greatly simplified BlastxMapping
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
switched test_blastx_serve
r
t
o us
e
new Tr
a
nslatio
n
DB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
C
h
r
i
stopher Lee
added re
a
d_blast
_
a
l
ignm
e
nt() transla
t
eDest o
p
tion
commit
|
commitdiff
|
tree
2009-07-16
C
hristopher Lee
added N
L
MSA
.
edges() method
commit
|
commitdiff
|
tree
2009-07-16
Christophe
r
L
e
e
s
w
itched test_tblastn_p
a
rse
r
to u
s
e n
e
w
Tran
s
lat
i
o
nDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christ
o
p
h
er Lee
s
w
itc
h
t
blastn to use new
T
r
anslationDB appr
o
ach
commit
|
commitdiff
|
tree
2009-07-15
Christophe
r
Lee
added translationDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
istopher
Lee
moved dbname default int
o
get_bound_subclass()
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
m
a
ke
CoordsTo
I
nterv
a
l
s / g
e
t_interva
l
() use seq
.
ab
s
ol
u
te_sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
cleaned up
S
eq
P
ath
.
clas
s
y
Sl
i
c
e(
)
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
pher Lee
Merge commit 'remote
s
/mkszu
b
a/nl
m
sa_no_ver
b
ose' in
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
stopher L
e
e
Merge commit 'remo
t
es/mks
z
uba/cn
e
stedlist_notice' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
C
hris
t
op
h
er Lee
incomplete new code for TranslationDB
commit
|
commitdiff
|
tree
2009-07-15
Christophe
r
Lee
cleaned up reversePath
construction
commit
|
commitdiff
|
tree
2009-07-15
Christopher
L
ee
add ab
s
o
l
ute_slice() m
e
thod
to SeqPath
commit
|
commitdiff
|
tree
2009-07-14
Christophe
r
Lee
Merge comm
i
t 'remotes/mkszuba/cnestedlis
t
_lo
g
ger' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
C
h
ristopher Lee
Mer
g
e
branch 'master' into meg
a
te
s
ts
commit
|
commitdiff
|
tree
2009-07-03
C
hristopher Le
e
Merge br
a
n
c
h 'f
o
rmatdb_fail'
commit
|
commitdiff
|
tree
2009-07-03
C
hristopher Lee
improve
d
whitespace
p
at
h
warning
commit
|
commitdiff
|
tree
2009-07-03
Christoph
e
r
L
ee
added warni
n
g for whitespa
c
e in path
commit
|
commitdiff
|
tree
2009-07-01
Chris
t
opher Lee
Merge c
o
mmit 'remotes/mkszuba/megatests'
commit
|
commitdiff
|
tree
2009-07-01
Chris
t
opher Lee
u
s
e glob
.
glob()
instead of
o
s
.
lis
t
d
i
r(); cleaned up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Christop
h
er Lee
Merge
com
m
i
t
'remotes/mkszu
b
a/mimetex
t
'
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
Mer
g
e
commit 'remotes/mkszuba
/
do
c
fix
e
s
'
commit
|
commitdiff
|
tree
2009-07-01
Chri
s
topher Lee
Merge
c
ommit 're
m
ote
s
/mksz
u
ba/hashlib'
commit
|
commitdiff
|
tree
2009-06-26
Chr
i
stophe
r
L
ee
f
i
xed
c
aching bug
i
ntroduced in com
m
it 8d9966 in Pre
f
ixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Chri
s
top
h
e
r Lee
deprecated cursor argum
e
nt to SQLTabl
e
commit
|
commitdiff
|
tree
2009-06-20
C
h
ristopher L
e
e
f
i
xed issue 99
commit
|
commitdiff
|
tree
2009-06-20
C
hristo
p
her Le
e
added test
f
o
r
issu
e
99
commit
|
commitdiff
|
tree
2009-06-20
Chri
s
t
o
pher
L
ee
cleaned up
S
QLite
S
e
rver
I
nfo
commit
|
commitdiff
|
tree
2009-06-20
Christophe
r
L
ee
add
e
d DBS
e
rverInfo
.
n
e
w_cur
s
o
r() method
commit
|
commitdiff
|
tree
2009-06-13
Christopher Lee
Mer
g
e commit 'remotes/
m
k
s
zuba/issu
e
9
7_test' into issue97_
t
est
commit
|
commitdiff
|
tree
2009-06-13
Ch
r
istopher Lee
removed redund
a
nt and buggy
rs
t
rip("
.
py
"
)
c
all from
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Christo
p
her
L
e
e
fix pyr
e
x cdef
commit
|
commitdiff
|
tree
2009-06-12
Ch
r
i
s
tophe
r
Lee
fix
issue97
commit
|
commitdiff
|
tree
2009-06-12
Christopher L
e
e
raised
minimum identit
y
for relaxed bl
a
s
t tests to 60%
commit
|
commitdiff
|
tree
2009-06-09
Chris
t
opher Lee
r
e
placed a few remaining
ref
s
in the docs to pyg
r
.
Data
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
C
h
r
istopher Lee
Merge commit 're
m
o
tes/mkszuba/deb'
commit
|
commitdiff
|
tree
2009-06-09
C
h
ri
s
toph
e
r Lee
Merge c
o
m
m
i
t 'rem
o
t
es/mkszuba/r
e
nam
e
s'
commit
|
commitdiff
|
tree
2009-06-09
Christop
h
er
Lee
M
e
rge branch '
i
nt
e
r
val_fi
l
ters
'
in
t
o blast_tests
commit
|
commitdiff
|
tree
2009-06-09
Christopher
Lee
r
e
laxed-
t
ests h
a
d a bug that made t
h
e
m pass the compari
s
on
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christo
p
her Lee
must close FilePo
p
en object before ex
i
ting BlastxMap
p
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chr
i
stopher Lee
merge
d
in ctb/blas
t
x_database
commit
|
commitdiff
|
tree
2009-06-04
Christoph
e
r Le
e
Merge com
m
it '
r
emotes/ctb/bla
s
tx_
g
enerato
r
' i
n
to ctb_tmp
commit
|
commitdiff
|
tree
2009-06-04
Christopher L
e
e
PEP8 and whitespa
c
e
fixes to nlmsa_ut
i
l
s
.
p
y; no
f
unctionali
t
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christopher
L
ee
converted add_al
i
gned_inte
r
vals function
a
l
i
t
y into
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chri
s
topher Lee
clea
n
up AttributeInt
e
rf
a
c
e according t
o
T
i
tus suggest
i
ons
commit
|
commitdiff
|
tree
2009-06-04
C
hristopher Lee
Merge commit 'remotes/ctb/ctb_intervals' int
o
inter
v
al_fil
t
ers
commit
|
commitdiff
|
tree
2009-06-03
Christo
p
her Lee
Merge
c
ommit '
r
emo
t
es/ctb/ctb_b
l
as
t
2' into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Ch
r
istopher Lee
M
e
r
g
e
commit 're
m
otes/
c
tb/minor_doc_fixes' into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Christoph
e
r Lee
merged in ctb/anno
t
ation
commit
|
commitdiff
|
tree
2009-06-03
Christophe
r
Lee
merged in
c
tb/blast_skip conflic
t
wi
t
h ctb/blast
_
cache
commit
|
commitdiff
|
tree
2009-06-03
Christopher Lee
Merge commit 'remote
s
/ctb/blast_cache' into ctb_
t
mp
commit
|
commitdiff
|
tree
2009-05-29
Christopher Lee
Merge commit 'remot
e
s/
c
t
b/nlmsa_iter_repr'
commit
|
commitdiff
|
tree
2009-05-29
Christophe
r
Lee
removed unnecessary
i
m
port
commit
|
commitdiff
|
tree
2009-05-29
Christo
p
h
er Lee
converted test_mult
i
blast_single() back
to t
e
st again
s
t
.
.
.
commit
|
commitdiff
|
tree
2009-05-29
Christophe
r
Lee
r
e
na
m
e to avoid false
implication this test involves
.
.
.
commit
|
commitdiff
|
tree
2009-05-27
Chri
s
topher
L
ee
Merge commi
t
'remote
s
/mks
z
ub
a
/trove' into mare
k
_
t
mp
commit
|
commitdiff
|
tree
2009-05-27
Christ
o
pher Lee
adde
d
comparison with single seq bl
a
st in test_multibl
a
s
t
commit
|
commitdiff
|
tree
2009-05-27
Chri
s
tophe
r
Lee
added text file f
o
r c
h
eck
i
ng long
p
arser res
u
lts
commit
|
commitdiff
|
tree
2009-05-27
Christoph
e
r
L
ee
put
cl
o
s
e
() within tr
y
-
f
inally
a
s al
w
ay
s
commit
|
commitdiff
|
tree
2009-05-27
Chris
t
op
h
er Lee
Mer
g
e comm
i
t 'remotes/mkszuba/blast_test'
i
nto ma
r
ek
_
tmp
commit
|
commitdiff
|
tree
2009-05-27
C
h
ristopher Lee
M
e
rge co
m
mit '
r
e
motes/mkszu
b
a/ebuilds
'
into marek_tmp
commit
|
commitdiff
|
tree
2009-05-23
Christ
o
p
h
er Lee
a
dded ResourceServer
r
egister() / serve_forever() docs
commit
|
commitdiff
|
tree
2009-05-23
Ch
r
istop
h
er Lee
u
se os
.
path
.
j
o
in() in detach_as_demon_proces
s
()
commit
|
commitdiff
|
tree
2009-05-23
Christo
p
her L
e
e
Merge commit 'remotes/m
k
szuba/blastx_com
m
ent' into
.
.
.
commit
|
commitdiff
|
tree
2009-05-22
Chri
s
t
o
pher Lee
fix
e
d pa
r
sing err
o
r in multiseq blast
commit
|
commitdiff
|
tree
2009-05-22
Christopher L
e
e
upda
t
ed
s
eqdb refer
e
nce docs for 0
.
8
commit
|
commitdiff
|
tree
2009-05-22
Christopher Lee
revised meta
b
ase / worldba
s
e re
f
e
rence docs f
o
r 0
.
8
.
.
.
commit
|
commitdiff
|
tree
2009-05-22
Ch
r
istop
h
er Lee
fix
e
d MetabaseList
.
reg
i
ster
S
erver(
)
commit
|
commitdiff
|
tree
2009-05-22
Christopher
L
ee
ad
d
e
d
l
i
st_pe
n
d
i
ng() to worldbase inte
r
f
a
c
e
commit
|
commitdiff
|
tree
2009-05-22
Christoph
e
r
L
ee
more revisions of
w
orldbas
e
and me
t
abase reference
.
.
.
commit
|
commitdiff
|
tree
2009-05-22
Chris
t
opher Lee
split off wo
r
l
d
b
ase r
e
ference docs for 0
.
8
commit
|
commitdiff
|
tree
2009-05-22
Christopher
L
ee
up
d
a
ted gui
d
elist to us
e
worldbase tutori
a
l
commit
|
commitdiff
|
tree
2009-05-22
Chr
i
stopher Le
e
rena
m
ed p
y
grdata
t
u
torial as worldbase
commit
|
commitdiff
|
tree
2009-05-22
Ch
r
ist
o
p
h
e
r Lee
revis
e
d mapping r
e
f docs fo
r
0
.
8
commit
|
commitdiff
|
tree
2009-05-22
Christopher
Lee
revised coordin
a
tor re
f
docs for 0
.
8
commit
|
commitdiff
|
tree
2009-05-22
Christopher
Le
e
r
e
vised cnestedlist
ref docs for 0
.
8
commit
|
commitdiff
|
tree
2009-05-22
Christopher Lee
revised classutil
r
ef docs f
o
r 0
.
8
commit
|
commitdiff
|
tree
2009-05-22
C
hristopher L
e
e
store blastx re
s
ults i
n
a
regular
Python list
commit
|
commitdiff
|
tree
2009-05-22
Ch
r
i
s
topher Lee
revised blast
reference docs
for
0
.
8
commit
|
commitdiff
|
tree
2009-05-22
C
h
ristopher Lee
revised anno
t
ation reference docs fo
r
0
.
8
commit
|
commitdiff
|
tree
2009-05-22
Christopher Le
e
made
A
nnotationDB
.
a
d
d_homology()
search argument non
.
.
.
commit
|
commitdiff
|
tree
2009-05-22
Christopher
Lee
ad
d
ed what
s
new t
o
table
of contents
commit
|
commitdiff
|
tree
2009-05-22
Christ
o
p
h
er
Lee
add
e
d
w
hatsnew
.
rst to D
o
cs
commit
|
commitdiff
|
tree
2009-05-22
Christopher Lee
re
m
o
v
ed obsolete F
a
s
taDB
commit
|
commitdiff
|
tree
2009-05-22
Christopher L
e
e
extend metab
a
s
e add_
r
esource
(
) met
h
od to accept a dictionary
.
.
.
commit
|
commitdiff
|
tree
2009-05-22
Christopher Lee
u
p
date
d
tutor
i
als for 0
.
8
commit
|
commitdiff
|
tree
2009-05-22
C
hristophe
r
Lee
fixed parsing error in multiseq
b
l
a
s
t
commit
|
commitdiff
|
tree
2009-05-22
Christopher
Lee
updated se
q
db
r
e
ference doc
s
f
o
r 0
.
8
commit
|
commitdiff
|
tree
2009-05-21
Christopher Lee
revis
e
d
m
e
tabase /
w
orldbase re
f
eren
c
e docs
f
or 0
.
8
.
.
.
commit
|
commitdiff
|
tree
2009-05-21
Christop
h
e
r Le
e
fixed Me
t
a
b
aseLi
s
t
.
re
g
isterServ
e
r()
commit
|
commitdiff
|
tree
2009-05-21
Christophe
r
Lee
added list_pend
i
ng() to wor
l
dba
s
e interface
commit
|
commitdiff
|
tree
2009-05-20
Christo
p
her Lee
more revisio
n
s of worldbase
and metabas
e
reference
.
.
.
commit
|
commitdiff
|
tree
2009-05-20
Christop
h
er Lee
s
p
lit of
f
world
b
ase r
e
ference docs for 0
.
8
commit
|
commitdiff
|
tree
2009-05-20
Chris
t
o
pher Lee
updated guideli
s
t
t
o use w
o
rldbase tut
o
ria
l
commit
|
commitdiff
|
tree
2009-05-20
C
hristopher Lee
renamed
pygrda
t
a tutor
i
a
l
as
w
orld
b
ase
commit
|
commitdiff
|
tree
2009-05-20
C
h
r
istopher Lee
r
e
vised mappi
n
g ref d
o
cs fo
r
0
.
8
commit
|
commitdiff
|
tree
next